Data on microsatellite markers in Colletotrichum gloeosporioides s.l., polymorphism levels and diversity range

Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2–29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.


a b s t r a c t
Colletotrichum gloeosporioides is a species complex of fungi belonging to the Glomerellaceae family (Ascomycota). It has a global worldwide occurrence and while sometimes described as a plant endophytic commensal, it also often demonstrates pathogenicity on crops and is responsible for anthracnose disease in many cultivated species. Thirty-nine polymorphic microsatellites were isolated and their polymorphism levels were determined in 95 strains from Guadeloupe (Lesser Antilles), mostly isolated from Water Yam (Dioscorea alata). The average allele number per polymorphic locus was 12.3 (decreasing to 4.3 at 5% frequency threshold, indicative of dramatic amounts of rare polymorphisms), with a range of 2-29 alleles. The microsatellite markers data will facilitate genetic diversity analyses and population genetics studies for the species complex.
& Type of data

Data
This dataset is a list of 39 microsatellite markers from the worldwide pathogenic species complex Colletotrichum gloeosporioides, including primers and basic information relative to diversity levels expected at each locus. Colletotrichum fungi are diversified [1], with species ranging from genuine endophytic commensals to biotrophic parasites or even saprophytic pathogens [2]. Species of this genus are thus often associated with crop diseases, and especially anthracnose in plants [3][4][5]. Taxonomic studies are currently investigating sequence based delineation of species (DNA barcoding, e.g. [6][7][8]), but reaching consensus is still undergoing [9]. Defining co-dominant and highly polymorphic molecular markers such as microsatellites available for diversity studies and cross geographical or ecological comparisons would be a valuable tool for the study of this species complex and would allow introducing genetic data complementary to the current genomic approaches [9]. Also, these markers might allow differentiating genetic pools that could reflect host adaptation or even possibly identify new species within strain pools (structuration via reduced gene flow, e.g. [6]). We successfully developed 39 microsatellite markers for this wide geographical and ecological range pathogen (Table 1).

Experimental design, materials and methods
Genomic DNA was extracted from seven strains of Colletotrichum gloeosporioides. Six microsatellite-enriched genomic libraries were produced following [10]. DNA was digested with RsaI and fragments of 500 bp were ligated into a pCR 4-TOPO vector. These were then used to transform One Shot TOP10 chemically competent Escherichia coli, producing a total of 1158 positives clones and 128 were sequenced on an ABI PRISM 3730XL automated sequencer, using T3 and T7 primers. Consensus sequences were obtained using ChromasPro 1.34 software [11]. Of these sequences, 21 were of poor quality, 24 did not show microsatellite region, 24 were sister clones, and 59 showed microsatellites (motifs of three repetitions or more). Forty-nine primers pairs were thus designed using Primer-3 [12] and PrimerSelect of DNAStar [13]. Table 1 Characteristics for the 39 study microsatellite loci. Probe accession reference can be retrieved at www.ncbi.nlm.nih.gov/probe/. Size range in bp, includes rare alleles of high size. #A is the number of alleles in our 95 strains. F 4x% is the number of alleles at a frequency higher than x% in the study sample. Ae is the efficient allele number (1/(1-Nei index)). In bold, 15  The primers were optimized for amplification, testing annealing temperature (44.5-64.2°C), MgCl2 concentration (1-3.5 mM), and polymerase chain reaction cycles (25-35). PCR conditions consisted of a denaturation stage at 95°C for 5 min followed by 40 cycles at 95°C for 30 s, 59°C for 30 s, 72°C for 30 s. Thirty-nine loci successfully amplified, all within expected sizes. In a further sample of 95 strains, polymorphism was assessed. High variability in alleles and Nei index were observed (Table 1). We report amplification success in single PCR runs, to help researchers chose loci more specifically. Indeed, Colletotrichum gloeosporioides demonstrate high phenotypic plasticity, possibly involving flexible DNA methylation, and amplification might vary depending on methylation state. We thus recommend choosing among these loci with a subsample study first.
In this polymorphism assessment, our strains were sampled from Dioscorea alata in Guadeloupe, where anthracnose is the main threat [14] and impacted agro-diversity [15]. Comparisons at wider geographical scales might enlighten important population processes: local dispersal [16], up to migration at greater scales [17], as well as genetic differentiation levels.